bbest
commented
10 years ago From: Ben Best bbest@nceas.ucsb.edu Date: Thu, Mar 27, 2014 at 3:36 PM Subject: Re: OHI Brazil findings launch plans To: Cristiane Elfes cristiane.elfes@lifesci.ucsb.edu Cc: Erich J Pacheco epacheco@conservation.org, Guilherme Dutra gdutra@conservation.org, Ana Cintia Guazzelli aguazzelli@conservation.org, Debra Zeyen d.zeyen@conservation.org, Ben Halpern halpern@bren.ucsb.edu, Katie Longo longo@nceas.ucsb.edu, Darren Hardy drh@stanford.edu, Courtney Scarborough scarborough@nceas.ucsb.edu, Tiago Pinheiro tcisalpino@gmail.com
Hi All,
The data has been linked from OHI-Science.org under the Data heading: Brazil 2013 (data). Please let me know if you notice any problems. In future we will fold these case study datasets directly into the toolbox.
Cheers, BB
PS Changes made here: /usr/local/ohi/src/model/bin/run_brazil_model.sh (diff)
####
# add documentation
# getting error:
# File "/usr/local/ohi/lib/python/ohi/__init__.py", line 50, in _loaddict
# return dict([(row['code'].lower(), row['name'].replace(' ', '-')) for row in csv.DictReader(open('%s/%s.csv' % (os.getenv('OHI_PARAMDIR'), k)))])
# IOError: [Errno 2] No such file or directory: '/var/lib/ohi/param/dimensions.csv'
# /var/data/ohi/usr/local/src/param/dimensions.csv
ln -s /var/data/ohi/usr/local/src/param/* /var/lib/ohi/param/.
vi /var/data/ohi/usr/local/src/param/regions.csv
#id,code,name
#1,gl,global # <- removed this line while running below for just Brazil
#2,br,brazil
echo "Generating documentation..."
test -r latex.cache && rm latex.cache
cd $OHI_HOME/src/model
export study=brazil
export OHI_STUDY=$study
# add README.txt so python ohi.doc populates with files
for d in `find ./brazil -type d -not -iwholename '*.svn*'`; do
if [ ! -f "$d/README.txt" ]; then
echo "$d/README.txt does NOT exist, touching for ohi.doc generation."
touch $d/README.txt
fi
done
python -m ohi.doc simple
python -m ohi.doc detailed
python -m ohi.doc lineage brazil
python bin/generate_lineage.py > ${study}/doc/sources.dot
bin/generate_sources_doc.sh
#python bin/dump_citations.py
echo "Auto-correcting terminology in documentation..."
for fn in ${study}*.markdown ${study}*.csv; do
echo " $fn"
sed -i \
-e 's/\bsustainability\b/resilience/g' \
-e 's/\bvulnerability\b/pressures/g' \
$fn
done
echo "Rendering documentation as HTML files..."
for fn in ${study}*.markdown; do
html_fn="`basename $fn .markdown`.html"
# see if our markdown output changed
if [ -d .svn/text-base ]; then
diff -q $fn .svn/text-base/${fn}.svn-base >/dev/null
if [ $? -eq 0 -a -f $html_fn ]; then
echo " No changes to $fn"
continue
fi
fi
# otherwise generate an html file if it's stale
if [ $fn -nt $html_fn -o ! -f $html_fn ]; then
echo " $fn"
ohi-markdown2html $fn $html_fn
fi
done
cd $OHI_HOME/src/model/brazil
# goals: psql -A -t -c 'select distinct g from global.results_goal'. also: /var/lib/ohi/param/goals.csv -> /var/data/ohi/usr/local/src/param/goals.csv
ln -s AO artisanal-fishing
ln -s BD biodiversity
ln -s CS carbon-storage
ln -s CW clean-waters
ln -s FP food-provision
ln -s LE livelihoods
ln -s NP natural-products
ln -s CP safe-coastlines
ln -s SP sense-of-place
ln -s TR tourism-and-recreation
# subgoals: psql -A -t -c 'select distinct g,c from global.results_component order by g,c' added: /var/lib/ohi/param/goals_subgoals.csv -> /var/data/ohi/usr/local/src/param/goals_subgoals.csv
ln -s HAB habitats
ln -s SPP species
ln -s FIS fishing
ln -s MAR mariculture
ln -s ECO economy
ln -s LIV livelihood
ln -s ICO iconic-species
ln -s LSP lasting-special-places
# make goals_subgoals.csv
dir_param=/var/data/ohi/usr/local/src/param
cp $dir_param/goals.csv $dir_param/goals_subgoals.csv
cat <<EOF >> /var/data/ohi/usr/local/src/param/goals_subgoals.csv
hab,habitats
spp,species
fis,fishing
mar,mariculture
eco,economy
liv,livelihood
ico,iconic-species
lsp,lasting-special-places
EOF
cat $dir_param/goals_subgoals.csv
ln -s $dir_param/goals_subgoals.csv /var/lib/ohi/param/.
cat ${OHI_PARAMDIR:-/var/lib/ohi/param}/goals_subgoals.csv | sed "1 d" | cut -d, -f2 # substitute line in bin/export_goal_data.sh
cd $OHI_HOME/src/model
bin/export_goal_data.sh
# NEXT: manually edit index.md from /Volumes/local_edit/src/model/brazil*.markdown
# and copy FROM index.md, doc, data, br_goaldata.zip -> data_goals TO /var/lib/ohi/www/data/br-2012
dir_ftp=/var/lib/ohi/www/data/br-2012
sudo chmod -R 775 $dir_ftp
sudo chgrp -R www-data $dir_ftp
sudo chown -R bbest $dir_ftp
ohi-markdown2html $dir_ftp/index.md $dir_ftp/index.html
z=$dir_ftp/`basename $dir_ftp`.zip
zip -r $z $dir_ftp -x $z
per Brazil layers request by Chris and Erich